BiSeq - betaResults output only contains chr1 and chr2
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@iscastanho-23170
Last seen 10 months ago

I am trying to run BiSeq on RRBS mouse datasets (~60 samples).

I just noticed that my betaResults output only contains chromosomes 1 and 2 (and consequently DMRs output) – does anyone know why this is? Is it because of the betaRegression() function? How could I include all chromosomes?

I have been following the tutorial / introduction (https://www.bioconductor.org/packages/release/bioc/vignettes/BiSeq/inst/doc/BiSeq.pdf) and adapting to my own data. This is however from 2015; does anyone know if there is a more recent tutorial for this?

Any experience / feedback / advice would be truly appreciated.

Thank you.

biseq betaRegression RRBS Methylation • 69 views
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You will have to provide much more information than that if you expect anybody to be able to help. Please provide relevant code that you used, and the output that shows you are only getting results from two chromosomes. Also remember to remove extraneous output from your code - for example those lines of R output where it is saying all the packages being loaded up - because you are limited to 5000 characters.

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